Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.
DOI:10.2210/pdb3kd1/pdb   NDB ID: NA0274
Primary Citation
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 115602.72
    Molecule: DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
    Polymer: 1 Type: dna Length: 18
    Chains: T
    Molecule: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3')
    Polymer: 2 Type: dna Length: 14
    Chains: P
    Fragment: Acyclic GMP terminated primer DNA
    Molecule: DNA polymerase
    Polymer: 3 Type: protein Length: 913
    Chains: E
    Fragment: RB69 gp43 exo- chimera containing elements from the fingers domain of the human cytomegalovirus DNA polymerase.
    Mutation: D222A V478W F479V N480S I557M N558A R559L L561V I562T I563C
    Organism: Enterobacteria phage RB69
    Gene Name: 43
    UniProtKB: Search PDB | Q38087   Protein Feature View
  •   Structure Validation Hide

    View the full validation report  


  • MolProbity Ramachandran Plot

  •   Related Citations in PDB Entry (REMARK 1) Hide
  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Enterobacteria phage rb69   Taxonomy   Common Name: Bacteriophage rb69 Expression System: Escherichia coli  
  •   Related PDB Entries Hide
    Identifier Details
    3KD5   Similar complex with phosphonoformic acid 
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG Mg
  •   Modified Residues Hide
    Identifier Formula Parent Type
    4DG C8 H12 N5 O6 P dna3PrimeTerminus
  •   External Domain Annotations Hide
  •   Structural Biology Knowledgebase Data Hide
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA0274
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
Downloadable viewers:
  •   MyPDB Personal Annotations Hide
  •   Deposition Summary Hide
    Authors:   Zahn, K.E.,  Doublie, S.

    Deposition:   2009-10-22
    Release:   2011-04-13
    Last Modified (REVDAT):   2015-04-15
  •   Revision History    Hide
    Mouse over text for details
    Version format compliance
  •   Experimental Details Hide
    Exp. Data:
      Structure Factors
    Resolution[Å]:   2.66
    R-Value: 0.212 (obs.)
    R-Free: 0.248
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 78.49 α = 90.00 
    b = 121.66 β = 90.00 
    c = 131.54 γ = 90.00